Shree Kumar Apte

Pyrroloquinoline-quinone: a reactive oxygen species scavenger in bacteria

Transgenic Escherichia coli expressing pyrroloquinoline‐quinone (PQQ) synthase gene from Deinococcus radiodurans showed superior survival during Rose Bengal induced oxidative stress. Such cells showed significantly low levels of protein carbonylation as compared to non‐transgenic control. In vitro, PQQ reacted with reactive oxygen species with rate constants comparable to other well known antioxidants, producing non‐reactive molecular products. PQQ also protected plasmid DNA and proteins from the oxidative damage caused by γ‐irradiation in solution. The data suggest that radioprotective/oxidative stress protective ability of PQQ in bacteria may be consequent to scavenging of reactive oxygen species per se and induction of other free radical scavenging mechanism.

The Kdp-ATPase system and its regulation

K+, the dominant intracellular cation, is required for various physiological processes like turgor homeostasis, pH regulation etc. Bacterial cells have evolved many diverse K+ transporters to maintain the desired concentration of internal K+. In E. coli, the KdpATPase (comprising of the KdpFABC complex), encoded by the kdpFABC operon, is an inducible high-affinity K+ transporter that is synthesised under conditions of severe K+ limitation or osmotic upshift. The E. coli kdp expression is transcriptionally regulated by the KdpD and KdpE proteins, which together constitute a typical bacterial two-component signal transduction system. The Kdp system is widely dispersed among the different classes of bacteria including the cyanobacteria. The ordering of the kdpA, kdpB and kdpC is relatively fixed but the kdpD/E genes show different arrangements in distantly related bacteria. Our studies have shown that the cyanobacterium Anabaena sp. strain L-31 possesses two kdp operons, kdp1 and kdp2, of which, the later is expressed under K+ deficiency and desiccation. Among the regulatory genes, the kdpD ORF of Anabaena L-31 is truncated when compared to the kdpD of other bacteria, while a kdpE-like gene is absent. The extremely radio-resistant bacterium, Deinococcus radiodurans strain R1, also shows the presence of a naturally short kdpD ORF similar to Anabaena in its kdp operon. The review elaborates the expression of bacterial kdp operons in response to various environmental stress conditions, with special emphasis on Anabaena. The possible mechanism(s) of regulation of the unique kdp operons from Anabaena and Deinococcus are also discussed.

Engineering of Deinococcus radiodurans R1 for Bioprecipitation of Uranium from Dilute Nuclear Waste

Genetic engineering of radiation-resistant organisms to recover radionuclides/heavy metals from radioactive wastes is an attractive proposition. We have constructed a Deinococcus radiodurans strain harboring phoN, a gene encoding a nonspecific acid phosphatase, obtained from a local isolate of Salmonella enterica serovar Typhi. The recombinant strain expressed an approximately 27-kDa active PhoN protein and efficiently precipitated over 90% of the uranium from a 0.8 mM uranyl nitrate solution in 6 h. The engineered strain retained uranium bioprecipitation ability even after exposure to 6 kGy of 60Co gamma rays. The PhoN-expressing D. radiodurans offers an effective and eco-friendly in situ approach to biorecovery of uranium from dilute nuclear waste.

Polyaniline-Based Highly Sensitive Microbial Biosensor for Selective Detection of Lindane

A highly sensitive, selective, and rapid, whole-cell-based electrochemical biosensor was developed for detection of the persistent organochlorine pesticide γ-hexachlorocyclohexane (γ-HCH), commonly known as lindane. The gene linA2 encoding the enzyme γ-hexachlorocyclohexane (HCH) dehydrochlorinase (LinA2), involved in the initial steps of lindane (γ-HCH) biotransformation, was cloned and overexpressed in Escherichia coli . The lindane-biodegrading E. coli cells were immobilized on polyaniline film. The rapid and selective degradation of lindane and concomitant generation of hydrochloric acid by the recombinant E. coli cells in the microenvironment of polyaniline led to a change in its conductivity, which was monitored by pulsed amperometry. The biosensor could detect lindane in the part-per-trillion concentration range with a linear response from 2 to 45 ppt. The sensor was found to be selective to all the isomers of hexachlorocyclohexane (HCH) and to pentachlorocyclohexane (PCCH) but did not respond to other aliphatic and aromatic chlorides or to the end product of lindane degradation, i.e., trichlorobenzene (TCB). The sensor also did not respond to other commonly used organochlorine pesticides like DDT and DDE. On the basis of experimental results, a rationale has been proposed for the excellent sensitivity of polyaniline as a pH sensor for detection of H(+) ions released in its microenvironment.

Preferential Utilization of Aromatic Compounds over Glucose by Pseudomonas putida CSV86

ABSTRACT Pseudomonas putida CSV86, a naphthalene-degrading organism, exhibited diauxic growth on aromatic compounds plus glucose, with utilization of aromatics in the first log phase and of glucose in the second log phase. Glucose supplementation did not suppress the activity of degrading enzymes, which were induced upon addition of aromatic compounds. The induction was inhibited by chloramphenicol, suggesting that de novo protein synthesis was essential. Cells showed cometabolism of aromatic compounds and organic acids; however, organic acids suppressed glucose utilization.

Uranium sequestration by a marine cyanobacterium, Synechococcus elongatus strain BDU/75042

A marine, unicellular cyanobacterium, Synechococcus elongatus strain BDU/75042 was found to sequester uranium from aqueous systems at pH 7.8. The organism could remove 72% (53.5 mg U g(-1) dry weight) of uranium from test solutions containing 100 microM uranyl carbonate within 1h. The equilibrium data fitted well in the Langmuir isotherm thus suggesting a monolayer adsorption of uranium on the cyanobacterial biomass and predicted the maximum adsorption capacity of 124 mg U g(-1) dry weight. Light and scanning electron microscopy coupled with energy dispersive X-ray fluorescence (EDXRF) spectroscopy confirmed the uranyl adsorption by this organism. Most of the bound uranium was found to be associated with the extracellular polysaccharides (EPS) suggesting its interaction with the surface active ligands. Fourier transform infrared (FT-IR) spectroscopy suggested the amide groups and the deprotonated carboxyl groups on the cyanobacterial cell surface were likely to be involved in uranyl adsorption. The cell bound uranium could be released by washing with ethylene diamine tetraacetic acid (EDTA) or 0.1N HCl. The X-ray diffraction (XRD) analyses revealed the identity of uranium deposits associated with the cell biomass as uranyl carbonate hydrate. The study revealed the potential of this cyanobacterium for harvesting uranium from natural aquatic environments.

Cloning and Overexpression of Alkaline Phosphatase PhoK from Sphingomonas sp. Strain BSAR-1 for Bioprecipitation of Uranium from Alkaline Solutions

ABSTRACT Cells of Sphingomonas sp. strain BSAR-1 constitutively expressed an alkaline phosphatase, which was also secreted in the extracellular medium. A null mutant lacking this alkaline phosphatase activity was isolated by Tn5 random mutagenesis. The corresponding gene, designated phoK, was cloned and overexpressed in Escherichia coli strain BL21(DE3). The resultant E. coli strain EK4 overexpressed cellular activity 55 times higher and secreted extracellular PhoK activity 13 times higher than did BSAR-1. The recombinant strain very rapidly precipitated >90% of input uranium in less than 2 h from alkaline solutions (pH, 9 ± 0.2) containing 0.5 to 5 mM of uranyl carbonate, compared to BSAR-1, which precipitated uranium in >7 h. In both strains BSAR-1 and EK4, precipitated uranium remained cell bound. The EK4 cells exhibited a much higher loading capacity of 3.8 g U/g dry weight in <2 h compared to only 1.5 g U/g dry weight in >7 h in BSAR-1. The data demonstrate the potential utility of genetically engineering PhoK for the bioprecipitation of uranium from alkaline solutions.

An exonuclease I-sensitive DNA repair pathway in Deinococcus radiodurans : a major determinant of radiation resistance

Deinococcus radiodurans R1 recovering from acute dose of γ radiation shows a biphasic mechanism of DNA double‐strand break repair. The possible involvement of microsequence homology‐dependent, or non‐homologous end joining type mechanisms during initial period followed by RecA‐dependent homologous recombination pathways has been suggested for the reconstruction of complete genomes in this microbe. We have exploited the known roles of exonuclease I in DNA recombination to elucidate the nature of recombination involved in DNA double‐strand break repair during post‐irradiation recovery of D. radiodurans. Transgenic Deinococcus cells expressing exonuclease I functions of Escherichia coli showed significant reduction in γ radiation radioresistance, while the resistance to far‐UV and hydrogen peroxide remained unaffected. The overexpression of E. coli exonuclease I in Deinococcus inhibited DNA double‐strand break repair. Such cells exhibited normal post‐irradiation expression kinetics of RecA, PprA and single‐stranded DNA‐binding proteins but lacked the divalent cation manganese [(Mn(II)]‐dependent protection from γ radiation. The results strongly suggest that 3′ (ρ) 5′ single‐stranded DNA ends constitute an important component in recombination pathway involved in DNA double‐strand break repair and that absence of sbcB from deinococcal genome may significantly aid its extreme radioresistance phenotype.

Gamma Radiation-induced Proteome of Deinococcus radiodurans Primarily Targets DNA Repair and Oxidative Stress Alleviation

The extraordinary radioresistance of Deinococcus radiodurans primarily originates from its efficient DNA repair ability. The kinetics of proteomic changes induced by a 6-kGy dose of gamma irradiation was mapped during the post-irradiation growth arrest phase by two-dimensional protein electrophoresis coupled with mass spectrometry. The results revealed that at least 37 proteins displayed either enhanced or de novo expression in the first 1 h of post-irradiation recovery. All of the radiation-responsive proteins were identified, and they belonged to the major functional categories of DNA repair, oxidative stress alleviation, and protein translation/folding. The dynamics of radiation-responsive protein levels throughout the growth arrest phase demonstrated (i) sequential up-regulation and processing of DNA repair proteins such as single-stranded DNA-binding protein (Ssb), DNA damage response protein A (DdrA), DNA damage response protein B (DdrB), pleiotropic protein promoting DNA repair (PprA), and recombinase A (RecA) substantiating stepwise genome restitution by different DNA repair pathways and (ii) concurrent early up-regulation of proteins involved in both DNA repair and oxidative stress alleviation. Among DNA repair proteins, Ssb was found to be the first and most abundant radiation-induced protein only to be followed by alternate Ssb, DdrB, indicating aggressive protection of single strand DNA fragments as the first line of defense by D. radiodurans, thereby preserving genetic information following radiation stress. The implications of both qualitative or quantitative and sequential or co-induction of radiation-responsive proteins for envisaged DNA repair mechanism in D. radiodurans are discussed.

Cloning of salinity stress-induced genes from the salt-tolerant nitrogen-fixing cyanobacterium Anabaena torulosa.

A subtractive hybridization procedure was used to clone genes of the cyanobacterium Anabaena torulosa expressed in response to salt stress. The method uses total RNA from salt-treated cells, labeled in vitro, as the probe. Hybridization to restriction digests of total DNA was used for interspecies comparison; the procedure was also successful for isolation of cosmids by colony hybridization, semiquantitative dot blots, and cosmid characterization by Southern blotting. Analysis of eleven independent cosmids containing genes whose transcription is abundantly induced by salt suggests that a substantial portion of the A. torulosa genome, probably in excess of 100 kilobases, responds to salt.